Artificial intelligence for imaging-based COVID-19 detection: Systematic review comparing added value of AI versus human readers.

PURPOSE: A growing number of studies have examined whether Artificial Intelligence (AI) systems can support imaging-based diagnosis of COVID-19-caused pneumonia, including both gains in diagnostic performance and speed. However, what is currently missing is a combined appreciation of studies comparing human readers and AI. METHODS: We followed PRISMA-DTA guidelines for our systematic review, searching EMBASE, PUBMED and Scopus databases. To gain insights into the potential value of AI methods, we focused on studies comparing the performance of human readers versus AI models or versus AI-supported human readings. RESULTS: Our search identified 1270 studies, of which 12 fulfilled specific selection criteria. Concerning diagnostic performance, in testing datasets reported sensitivity was 42-100% (human readers, n = 9 studies), 60-95% (AI systems, n = 10) and 81-98% (AI-supported readers, n = 3), whilst reported specificity was 26-100% (human readers, n = 8), 61-96% (AI systems, n = 10) and 78-99% (AI-supported readings, n = 2). One study highlighted the potential of AI-supported readings for the assessment of lung lesion burden changes, whilst two studies indicated potential time savings for detection with AI. CONCLUSIONS: Our review indicates that AI systems or AI-supported human readings show less performance variability (interquartile range) in general, and may support the differentiation of COVID-19 pneumonia from other forms of pneumonia when used in high-prevalence and symptomatic populations. However, inconsistencies related to study design, reporting of data, areas of risk of bias, as well as limitations of statistical analyses complicate clear conclusions. We therefore support efforts for developing critical elements of study design when assessing the value of AI for diagnostic imaging.

Assessing the safety and efficacy of TAVR compared to SAVR in low-to-intermediate surgical risk patients with aortic valve stenosis: An overview of reviews.

BACKGROUND: Transcatheter aortic valve replacement (TAVR) was initially introduced to treat patients with aortic valve stenosis (AS) at high-risk for surgical aortic valve replacement (SAVR). Today, there is ample evidence supporting TAVR in high-risk groups. However, in recent years TAVR has been extended to low-to intermediate risk groups and relevant clinical evidence is still emerging, leaving some uncertainties. METHODS: To obtain information on TAVR versus SAVR in low-to intermediate risk groups, we conducted an overview of systematic reviews following PRISMA guidelines and based on a systematic search of EMBASE, MEDLINE, Cochrane and CRD databases. We focused on systematic reviews assessing mortality and VARC 2 as clinical outcomes. RESULTS: The majority of the 11 systematic reviews included in our study reported no differences in mortality between TAVR and SAVR at short and long-term follow-up times. Two reviews that included the most recent RCTs on low-risk patients reported a decreased mortality risk with TAVR at one-year follow-up. Regarding the secondary endpoints of stroke and MI, the majority of studies presented similar results for TAVR and SAVR. Acute Kidney Injury, Bleeding Complications, Atrial Fibrillation were less frequent with TAVR, with lower risk of Permanent Pacemaker Implantation and Aortic Regurgitation with SAVR. CONCLUSIONS: Our overview indicated that TAVR is a promising intervention for low-to-intermediate surgical risk patients; however additional evidence from longer term follow-up is needed to confirm these findings. This overview highlights inconsistencies about reporting and presentation of data, most notably limited clarity on effects of risk of bias on trial results.

Collaboration of the Joint Research Centre and European Customs Laboratories for the Identification of New Psychoactive Substances.

BACKGROUND: The emergence of psychoactive designer drugs has significantly increased over the last few years. Customs officials are responsible for the control of products entering the European Union (EU) market. This control applies to chemicals in general, pharmaceutical products and medicines. Numerous products imported from non-EU countries, often declared as 'bath salts' or 'fertilizers', contain new psychoactive substance (NPS). REVIEW: These are not necessarily controlled under international law, but may be subject to monitoring in agreement with EU legislation. This situation imposes substantial challenges, for example, for the maintenance of spectral libraries used for their detection by designated laboratories. The chemical identification of new substances, with the use of powerful instrumentation, and the time needed for detailed analysis and interpretation of the results, demands considerable commitment. The EU Joint Research Centre endeavors to provide scientific support to EU Customs laboratories to facilitate rapid identification and characterisation of seized samples. In addition to analysing known NPS, several new chemical entities have also been identified. Frequently, these belong to NPS classes already notified to the European Monitoring Centre for Drugs and Drug Addiction (EMCDDA) by the European Early- Warning System (EWS). CONCLUSION: The aim of this paper is to discuss the implementation of workflow mechanisms that are in place in order to facilitate the monitoring, communication and management of analytical data. The rapid dissemination of this information between control authorities strives to help protect EU citizens against the health risks posed by harmful substances.

Proteomics study of silver nanoparticles on Caco-2 cells.

Silver nanoparticles (AgNPs) have been incorporated into several consumer products. While these advances in technology are promising and exciting, the effects of these nanoparticles have not equally been studied. Due to the size, AgNPs can penetrate the body through oral exposure and reach the gastrointestinal tract. The present study was designed as a comparative proteomic analysis of Caco-2 cells, used as an in vitro model of the small intestine, exposed to 30 nm citrate stabilized-silver nanoparticles (AgNPs) for 24 or 72 h. Using two complementary proteomic approaches, 2D gel-based and label-free mass spectrometry, we present insight into the effects of AgNPs at proteins level. Exposure of 1 or 10 µg/mL AgNPs to Caco-2 cells resulted in 56 and 88 altered proteins at 24 h and 72 h respectively, by 2D gel-based technique. Ten of these proteins were found to be common between the two time-points. Using label-free mass spectrometry technique, 291 and 179 altered proteins were found at 24 h and 72 h, of which 24 were in common. Analysis of the proteomes showed several major biological processes altered, from which, cell cycle, cell morphology, cellular function and maintenance were the most affected.

Systematic analytical characterization of new psychoactive substances: A case study.

New psychoactive substances (NPS) are synthesized compounds that are not usually covered by European and/or international laws. With a slight alteration in the chemical structure of existing illegal substances registered in the European Union (EU), these NPS circumvent existing controls and are thus referred to as "legal highs". They are becoming increasingly available and can easily be purchased through both the internet and other means (smart shops). Thus, it is essential that the identification of NPS keeps up with this rapidly evolving market. In this case study, the Belgian Customs authorities apprehended a parcel, originating from China, containing two samples, declared as being "white pigments". For routine identification, the Belgian Customs Laboratory first analysed both samples by gas-chromatography mass-spectrometry and Fourier-Transform Infrared spectroscopy. The information obtained by these techniques is essential and can give an indication of the chemical structure of an unknown substance but not the complete identification of its structure. To bridge this gap, scientific and technical support is ensured by the Joint Research Centre (JRC) to the European Commission Directorate General for Taxation and Customs Unions (DG TAXUD) and the Customs Laboratory European Network (CLEN) through an Administrative Arrangement for fast recognition of NPS and identification of unknown chemicals. The samples were sent to the JRC for a complete characterization using advanced techniques and chemoinformatic tools. The aim of this study was also to encourage the development of a science-based policy driven approach on NPS. These samples were fully characterized and identified as 5F-AMB and PX-3 using (1)H and (13)C nuclear magnetic resonance (NMR), high-resolution tandem mass-spectrometry (HR-MS/MS) and Raman spectroscopy. A chemoinformatic platform was used to manage, unify analytical data from multiple techniques and instruments, and combine it with chemical and structural information.

A combined proteomics and metabolomics approach to assess the effects of gold nanoparticles in vitro.

Omics technologies, such as proteomics or metabolomics, have to date been applied in the field of nanomaterial safety assessment to a limited extent. To address this dearth, we developed an integrated approach combining the two techniques to study the effects of two sizes, 5 and 30 nm, of gold nanoparticles (AuNPs) in Caco-2 cells. We observed differences in cells exposed for 72 h to each size of AuNPs: 61 responsive (up/down-regulated) proteins were identified and 35 metabolites in the cell extract were tentatively annotated. Several altered biological pathways were highlighted by integrating the obtained multi-omics data with bioinformatic tools. This provided a unique set of molecular information on the effects of nanomaterials at cellular level. This information was supported by complementary data obtained by immunochemistry, microscopic analysis, and multiplexed assays. A part from increasing our knowledge on how the cellular processes and pathways are affected by nanomaterials (NMs), these findings could be used to identify specific biomarkers of toxicity or to support the safe-by-design concept in the development of new nanomedicines.

Can we trust untargeted metabolomics? Results of the metabo-ring initiative, a large-scale, multi-instrument inter-laboratory study.

The metabo-ring initiative brought together five nuclear magnetic resonance instruments (NMR) and 11 different mass spectrometers with the objective of assessing the reliability of untargeted metabolomics approaches in obtaining comparable metabolomics profiles. This was estimated by measuring the proportion of common spectral information extracted from the different LCMS and NMR platforms. Biological samples obtained from 2 different conditions were analysed by the partners using their own in-house protocols. Test #1 examined urine samples from adult volunteers either spiked or not spiked with 32 metabolite standards. Test #2 involved a low biological contrast situation comparing the plasma of rats fed a diet either supplemented or not with vitamin D. The spectral information from each instrument was assembled into separate statistical blocks. Correlations between blocks (e.g., instruments) were examined (RV coefficients) along with the structure of the common spectral information (common components and specific weights analysis). In addition, in Test #1, an outlier individual was blindly introduced, and its identification by the various platforms was evaluated. Despite large differences in the number of spectral features produced after post-processing and the heterogeneity of the analytical conditions and the data treatment, the spectral information both within (NMR and LCMS) and across methods (NMR vs. LCMS) was highly convergent (from 64 to 91 % on average). No effect of the LCMS instrumentation (TOF, QTOF, LTQ-Orbitrap) was noted. The outlier individual was best detected and characterised by LCMS instruments. In conclusion, untargeted metabolomics analyses report consistent information within and across instruments of various technologies, even without prior standardisation.

Mechanism of cisplatin proximal tubule toxicity revealed by integrating transcriptomics, proteomics, metabolomics and biokinetics.

Cisplatin is one of the most widely used chemotherapeutic agents for the treatment of solid tumours. The major dose-limiting factor is nephrotoxicity, in particular in the proximal tubule. Here, we use an integrated omics approach, including transcriptomics, proteomics and metabolomics coupled to biokinetics to identify cell stress response pathways induced by cisplatin. The human renal proximal tubular cell line RPTEC/TERT1 was treated with sub-cytotoxic concentrations of cisplatin (0.5 and 2 µM) in a daily repeat dose treating regime for up to 14 days. Biokinetic analysis showed that cisplatin was taken up from the basolateral compartment, transported to the apical compartment, and accumulated in cells over time. This is in line with basolateral uptake of cisplatin via organic cation transporter 2 and bioactivation via gamma-glutamyl transpeptidase located on the apical side of proximal tubular cells. Cisplatin affected several pathways including, p53 signalling, Nrf2 mediated oxidative stress response, mitochondrial processes, mTOR and AMPK signalling. In addition, we identified novel pathways changed by cisplatin, including eIF2 signalling, actin nucleation via the ARP/WASP complex and regulation of cell polarization. In conclusion, using an integrated omic approach together with biokinetics we have identified both novel and established mechanisms of cisplatin toxicity.

A proteomic approach to investigate AuNPs effects in Balb/3T3 cells.

Although gold nanoparticles (AuNPs) are currently used in several industrial products and biomedical applications, information about their biological effects is very limited. Thus, it is becoming crucial to assess their safety and adequately investigate the complexity of cell-nanoparticles interactions. In this work, the Balb/3T3 mouse fibroblast cell line was selected as an in vitro model to study the effects of AuNPs. Alteration of cellular processes and biochemical pathways caused by AuNPs exposure was investigated by analysing the differentially expressed proteome. Of interest was the difference observed in the protein pattern expression of cells exposed to AuNPs. It was found that 88 and 83 proteins were de-regulated after exposure to 5 and 15nm AuNPs, respectively. Analysis of the proteome revealed that AuNPs triggers several pathways related to cellular growth and proliferation, cell morphology, cell cycle regulation, cellular function and maintenance, oxidative stress, and inflammatory response. Moreover, SPR analysis showed an increase of ECM proteins biosynthesis in cells exposed to AuNPs. We observed by TEM analysis that NPs are internalized and confined mainly in autophagosomes. Endoplasmic reticulum stressed and modification at mitochondrial level occurred. This study aims to improve existing knowledge necessary for a correct assessment of the balance between AuNPs potential adverse and beneficial effects and might have important implications for biomedical applications (e.g. nanomedicine). To conclude proteomics link to system biology analysis is a valuable tool to understand and predict nanoparticles' toxicity, furthermore it has the potential to reveal pathways that may not be immediately evident with classical toxicological assays.

Analytical methods for detection of gluten in food--method developments in support of food labeling legislation.

The current essential therapy of celiac disease is a strict adherence to a gluten-free diet. Besides food products that are naturally gluten-free, "very low gluten" and "gluten-free" bakery products have become available. The availability of immunochemical and other analytical methods to determine gluten markers in foods is of utmost importance to ensure the well being of gluten-sensitive individuals. The aim of this review was to evaluate if currently available methodologies are suitable to meet the requirements of food labeling standards for individual gluten source declaration, in order to achieve policy objectives. Codex Alimentarius and European Union (EU) legislation and gluten detection methodologies applicable at present have been summarized and compared. In 2009, the European Commission issued Regulation No. 41/2009 concerning the composition and labeling of foodstuffs suitable for people intolerant to gluten. This review constitutes a basis to investigate the possibility to develop a proteomic-based method for the specific detection of gluten-containing cereals in food products, especially at or around the limits specified in EU legislation.

Development of a real-time PCR method for the simultaneous detection of soya and lupin mitochondrial DNA as markers for the presence of allergens in processed food.

Lupin and soya are members of the Leguminosae family which are recognised as some of the richest source of vegetable proteins. Lupin- and soya-containing products are available on the EU market and could cause severe adverse reactions in allergic individuals, even if consumed at low concentrations. In this context the development of methods for reliable detection of these allergens in food products is a useful tool for the surveillance of established legislation on food labelling within the EU. This work described the development of a duplex real-time PCR method allowing the simultaneous detection of traces of lupin and soya in processed food based on a specific TaqMan® probe designed on a mitochondrial tRNA-MET gene. A set of primers and probes was designed for the amplification of a 168 and 175bp fragment of lupin and soya mitochondrial DNA, respectively. The performance of the method was established using lupin and soya flours and cookies baked from lupin- and soya-containing dough (different concentrations and baking times). The PCR platform yielded consistent and repeatable results. The specificity of the system was tested with DNA from 28 plant species. The sensitivity of the method was suitable to detect allergenic ingredients in the low mg per kg range. Both lupin and soya at a level of 2.5mg per kg food matrix could be detected in cookies baked at 180°C for 10min. The method was successfully applied to bakery (e.g. bread) and vegetarian (e.g. non-meat sausages) food products that contain or may contain soya and/or lupin as ingredient or contaminant (according to the declaration on the product label).

Resolution and identification of major peanut allergens using a combination of fluorescence two-dimensional differential gel electrophoresis, Western blotting and Q-TOF mass spectrometry.

Peanut allergy is triggered by several proteins known as allergens. In this study, the complexity the peanut allergome is investigated with proteomic tools. The strength of this investigation resides in combining the high-resolving power and reproducibility of fluorescence two-dimensional differential gel electrophoresis with specific immunological detection as well as polypeptide sequencing by high-resolution mass spectrometry. Matching of the peanut proteins in 2D gels was achieved by differential labelling whereby peanut proteins and purified allergens (Ara h 1, Ara h 2 or Ara h 3/4) were run on the same gel. Ten protein spots on a mass line of ca. 63-68 kDa were likely to correspond to Ara h 1. Two doublets on two different mass lines at ca. 16 and 18 kDa matched with purified allergen Ara h 2. The basic and acidic sub-units of Ara h 3/4 were observed at masses of ca. 25 kDa and 40-45 kDa, respectively. Subsequently the antibody-binding capacity of spots corresponding to peanut allergens was investigated by Western blotting of 2D gels using antibodies (IgY) raised against Ara h 1, Ara h 2 and the recombinant 40 kDa sub-unit of Ara h 3/4. Final confirmation of the identity of the protein spots matched after 2D electrophoresis and identified by Western blotting was obtained by in-gel digestion of protein spots and analysis by quadrupole time-of-flight mass spectrometry. By using the method developed in our work, the location and identification of two different isoforms of the allergen Ara h 1, the allergen Ara h 2 and six isoforms of the allergen Ara h 3/4 in 2D peanut protein maps was established.

Proteomics-based approach to detect and identify major allergens in processed peanuts by capillary LC-Q-TOF (MS/MS).

An MS-based method, combining reversed-phase capillary liquid chromatography (capillary LC) with quadrupole time-of-flight tandem mass spectrometry (nano-ESI Q-TOF MS/MS), was developed with the aim of identifying a set of peptides that can function as markers for peanut allergens. Emphasis was given to the identification of the three major peanut allergens Ara h 1, Ara h 2, and Ara h 3, because these proteins are considered to represent >30% of the total protein content of peanut and are directly relevant for the allergenic potential of this food. The analytical data obtained were used to perform databank searching in combination with de novo sequencing and led to the identification of a multitude of sequence tags for all three peanut allergens. Food processing such as roasting of peanuts is known to affect the stability of proteins and was shown to influence the detection of allergen sequence tags. The analysis of raw and roasted peanuts allowed the identification of five peanut-specific sequence tags that can function as markers of the specific allergenic proteins. For Ara h 1, two peptide markers were proposed, namely, VLEENAGGEQEER (m/z 786.88, charge 2+) and DLAFPGSGEQVEK (m/z 688.85, charge 2+), whereas for Ara h 2 only one peptide, RQQWELQGDR (m/z 439.23, charge 3+), was found to satisfy the required conditions. For Ara h 3, the two specific peptides, SPDIYNPQAGSLK (m/z 695.35, charge 2+) and SQSENFEYVAFK (m/z 724.84, charge 2+), were selected. Other peptides have been proposed as indicative for food processing.